


Freedom of Choice

by rabidfan



Category: Stargate Atlantis
Genre: Gen
Language: English
Status: Completed
Published: 2015-01-10
Updated: 2015-01-10
Packaged: 2018-03-07 00:41:25
Rating: Not Rated
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 3,695
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/3154385
Author URL: https://archiveofourown.org/users/rabidfan/pseuds/rabidfan
Summary: <blockquote class="userstuff">
              <p>He’d been given a direct order.  No rescue was to be attempted.  They were <i>covert</i>, and as such no one was to know they were watching as two rescue helicopters went down over the mountains of Afghanistan.  It didn’t matter that John could hear the pilot desperately calling for help.  Orders were orders.  Observe and report.</p>
            </blockquote>





	Freedom of Choice

**Author's Note:**

  * For [StarbucksSue](https://archiveofourown.org/users/StarbucksSue/gifts).



> Sue was very supportive of my angst when my computer ate my original story. She said my recipient would understand and appreciate the story I ended up with. Gosh, I sure hope she was right!

~*~

Sitting in the crowded hangar gave John unwanted time to consider the ruins of his once promising career. He’d been given a direct order. No rescue was to be attempted. They were _covert_ , and as such no one was to know they were watching as two rescue helicopters went down over the mountains of Afghanistan. It didn’t matter that John could hear the pilot desperately calling for help. Orders were orders. Observe and report.

It wasn’t an order that John could in good conscience obey. And Holland would be alive to send Christmas cards to him in Leavenworth…so it was worth it. John was almost (possibly) certain that alone made the immolation of his career worthwhile. Looking around at his fellow prisoners lined up waiting for transport, he had to wonder what had caused the end of _their_ careers and if they thought it was worth the cost as well. With a sigh he settled in. One thing the military had taught him was how to wait. He didn’t like it, but he was good at it.

He’d once had dreams of making general. It was laughable now, but he’d believed he could do it. Standing before his angry father, he’d announced just that. _Can you see me now, Dad?_ , he thought.

Dad had always said he was a screw up.

The CIA had made it clear. There would be no trial. The Air Force, the public and the other branches of the government would never know the details of the mission or its fallout. He was the designated fall guy and he was going to obediently fall on his sword like a proper Airman.

John looked down at the shackles on his wrists and ankles and sighed. He’d been given a choice. A twenty year stretch in a military prison or a five year term of indentured servitude. He’d been pretty sure once he’d entered prison he’d never see the light of day again. Flipping a coin, he’d opted for servitude. Looking up at the security forces in their riot gear and brandishing pain sticks he was beginning to have second thoughts. Sighing, he shuffled to his feet to join the line leading to the plane that would take him to his new “master”. Leavenworth was sounding better and better.

~*~

The last of the prisoners heading for Leavenworth had long since left the plane. John and four others sat, waiting for the controllers that would come to claim them. Paperwork filled out, the SF’s began calling names one by one, handing the remaining prisoners over to those with the legal right to claim them. Finally there was only John.

There was only John for a long time.

Finally, John heard a pissy-sounding voice outside the plane. The SF by the exit gestured with his pain stick for John to stand. “You’re gonna love this guy.”

Sighing, John shuffled forward. He sounded charming. “If we could speed up, people? Wasting valuable time here.”

Yup. Charming.

Standing next to the plane was a stocky man dressed in an expensive suit. Crooked mouth, receding hairline, arms crossed belligerently over his chest. “Major. My name is Doctor Rodney McKay. I’ll be taking charge of you for the time being. This way, please.” He gestured towards the large SUV standing a few yards away.

“Chop, chop, major. We’re on a schedule here. We need to get back to the mountain.”

Mountain? John looked around him. There were certainly mountains surrounding them. He wasn’t sure where they were. Montana? Colorado? Shrugging it off for the moment, John struggled to get into the vehicle. His shackles kept catching on the seat belt and door hardware. The sergeant waiting for him knelt down and gathered the chain between his ankle restraints into his hands. Settling John into the backseat, he reached across his chest to draw the seatbelt across and secure it. He smiled, warm and genuine. “All set?”

Shocked speechless, John could do nothing but nod. “Right, then.” Standing, (Stackhouse, according to the name plate on his jacket) he closed the door for John and slid into the front seat.

“If we’re finally ready?” Rodney glared. Flipping open his tablet, he then ignored all the occupants of the vehicle. John leaned back, resting his head against the back of the seat. Closing his eyes, he allowed himself to drift. He was safe for now.

~*~

Sitting in the infirmary waiting for the doctor to finish his physical, John felt a strange ‘itch’ in the back of his head. The doctor pulled a small, rectangular object from a pocket. The itch he’d felt since his arrival at the mountain (and what a disappointment that was. Underground instead of on a snow peak. Bummer) racked up to nearly unbearable proportions. Reaching out to touch the unit the doctor still held he was surprised when the doctor wrenched it back out of reach.

The sudden movement brought the SF’s standing at the doorway into the room, pain sticks raised. “No, it’s okay. Relax, gentlemen. I don’t want him interacting with ancient tech until Doctor McKay arrives. He’d never let me live it down if we started without him.”

Smiling in rueful agreement, the SF’s lowered their sticks and stepped back to the doorway only to be shoved aside as Rodney pushed into the room.

“Sheppard. Dr. Lam. I’m sorry I’m late. I’m surrounded by morons.” Flicking his eyes to John he continued, “Are we ready to test his gene’s strength?”

“Ready, Doctor.” Carolyn handed the scanner to Rodney. “Do the honors?”

Rodney rolled his eyes. Handing the unit to John he said, “Major, concentrate on this device. Try to imagine its purpose.”

Eyebrow climbing up his forehead, John reached over to claim the small device. He held it steady even when it lit up, a trait Rodney appreciated in anyone handling delicate Ancient technology. 

“What does the device do, John?”

“It’s a scanner to gauge structural integrity.” Rodney’s disappointment was palpable. All the effort to retrieve John was wasted. Rodney startled when John continued.

“That’s not what you’re using it for, though. You’re using it as a medical device…gauging bone density?”

Rodney grinned. He looked to Dr. Lam for confirmation but he already knew all the effort had indeed been worth it. John had the ATA gene in spades.

“He’s right. We use it to measure the progress of healing in complex fractures and other bone injuries.” She leaned over to retrieve the scanner. “Major, I’d say you have a very powerful expression of the Ancient gene. Congratulations.”

“Ancient gene?”

“I’ll let Dr. McKay explain everything from this point on.” Smiling, she patted John’s knee. “You’re free to go, major. Keep up with the diet I’ve prescribed for you. I want to see you put some pounds on.”

“Sure thing, Doc.” John slid off the table. “Thanks.”

Giving Rodney one last, measured look, Carolyn headed off to her tiny office.

“What was that look about? What did that voodoo practitioner think I did this time?”

John smirked. “Don’t look at me. I just got here.”

Rodney huffed. “Fine. Let’s go. I’m starving and clearly you need to eat.” Snapping his fingers, Rodney burst out, “That’s it. She’s convinced I’ll forget to feed you. The nerve. I’ll have you know I’m a genius. I have a cat. I take very good care of Waldo, I assure you. I never forget to feed her.”

“I’m not a cat, McKay.” What the hell? He named his female cat Waldo? “I’m not a pet and I’m perfectly capable of feeding myself.”

“What? No! That’s not what I meant.” Rodney frowned. “You know what? Never mind. Let’s just go get something to eat.”

John sighed when the SF’s fell into step behind them.

~*~

Shifting a wary glance at the guards outside the lab door, John shifted on the stool he’d been perched on for what seemed like _years_. The lighter weight restraints he’d been fitted with helped the fatigue factor but he still tired easily. “My ass is numb, Doctor. Can we take a break?” Playing to Rodney’s fear of Doctor Lam he added, “I’m hungry.”

Rodney looked up from the circle of computer monitors surrounding him. “We’ve only just started, Sheppard…” looking at his watch he was startled to find over six hours had passed. The witch doctor was going to kill him, he thought. “Or maybe not. Fine.” He began shutting down the computers one by one. Once he’d packed away his tablet and papers he headed for the door. “Let’s go.”

“Awesome.” John stood and stretched his back to ease the kinks that had formed over the hours hunched over the gewgaws Rodney had had him laying his hands on.

“Heading out, gentlemen?”

John shot to attention. “General O’Neill, sir.” He fumbled through a half-assed salute.

“Relax Sheppard. You’re among friends. No need to stick to protocol around here.”

“Sir.” John repeated but allowed himself to relax somewhat into parade rest.

“Doctor McKay.” General O’Neill shifted over to pick up on of the items lining the desk behind him. “What do these Ancient gizmos do, Sheppard?”

Before John could formulate a reply Rodney rushed over to remove the item from the general’s hand. “Please stop touching things, general. You know how much trouble that gets us into. Now. We’re heading to the mess. John is hungry.” Rodney’s brain abruptly caught up with his mouth and decided it wasn’t a good idea to annoy the man currently in charge of the Atlantis mission. “Was there something you wanted? Something I can do for you?”

Smirking at John, O’Neill settled against the desk. “Yeah. About that. I’ve had people looking into your arrest and trial, Sheppard. Funny thing is? There’s no record of a trial. Odd, don’t you think?” His hands started drifting towards the Ancient tech again. “So I now have some answers….but I’ve got twice as many questions. I’m keeping them at it, though.” O’Neill straightened. Tapping the side of his nose he said, “The whole thing smells of a cover up. I hate that. So.” He headed for the door. “Who wants pie?”

Bemused, John followed the general to the elevator.

Once the doors had closed and they’d begun their slow climb towards the mess hall, O’Neill spoke again.

“I’m pretty sure I can get your sentence reduced, Sheppard. Maybe even expunged all together. Just give me some time.”

Rodney had a moment of panic. If Sheppard’s record was cleared he’d no longer be required to go to Pegasus with Rodney. His expression of ATA gene was vital to their success. With that thought Rodney sighed. He didn’t want to own Sheppard. He didn’t want _anyone_ to own Sheppard. He found the idea of slavery for any reason repugnant. He wouldn’t stand in the way of John’s freedom no matter how important he was to Rodney’s mission.

The three entered the mess and headed to the steam tables to make their selections. “Will the inquiry hold up our departure, general?”

“Doubtful, Doctor McKay. We can keep at it even after launch. It’s not like you’re cut off from us anymore.”

“Departure? Launch?” John looked from one man to the other.

O’Neill pinched the bridge of his nose and resisted (barely) punching McKay in his.

“Is there a reason why you’ve held back explaining things to the major, McKay?”

“Have you any idea how much work I need to do before launch? How unbelievably helpful the major’s gene strength is to that work? Work I could be accomplishing this very moment if I wasn’t trapped here wasting valuable time. The discoveries I’m not making right now could mean death to thousands…no… _millions_ of people. I do not have time to explain the history of the Stargate program.”

Sheppard and O’Neill both leaned back out of the path of Rodney’s flailing limbs.

“Fact, McKay. Sheppard, through no fault of his own, belongs to you until I say otherwise. Fact. His position on the Atlantis expedition is contingent on my approval. Fact. No one is launching without receiving full disclosure and giving their willing agreement to take part in the expedition. That includes Major Sheppard. So. Find the time today, McKay or I’ll find someone else to hold the major’s parole.”

Nodding once to Sheppard O’Neill headed back the way they’d come.

~*~

“So. Let me see if I’ve got this right. There’s a big metal ring that opens a wormhole between planets. The ancient people whose gene I’ve got built the thing and also the lost city of Atlantis. Only it’s not lost…it’s on another planet. In another galaxy. And we’re going there in a spaceship built by the Roswell greys. That the gist?”

Rodney rocked on his toes, proud of John’s recall. “Asgard. They’re Asgard. But essentially? That’s the gist.” Frowning in thought he concluded, “The Daedalus is more of a hybrid, you know. Earth/Asgard technology combined.”

“Of course.” John sighed. “Rodney, you know you people are bat-shit insane, right?”

Rodney grinned. “You think so? We’ll see.”

~*~

“General, you simply can’t overlook the law. Major Sheppard has been sentenced to a term of servitude and you must accept that.” Richard Woolsey sniffed. He hated dealing with the military types. “He’s served less than six months of his five year parole. His gene status cannot subvert justice. He simply cannot go to Pegasus without a registered owner and military restraints.”

“Justice.” Jack sat back in his chair and favored the bureaucrat with a glare. “What exactly do you know about justice?” Pushing back from the table, he stood and strode across the room to lean over Woolsey. “The major wasn’t given a trial, his case wasn’t seen by a military tribunal. That? Would have resulted in something I could have accepted as justice.”

Sighing, he stepped back. He _needed_ Woolsey on his side. Losing it and attacking him was not the way to achieve that. “Richard. You and I both know what the CIA is capable of. We know all too well that they are not above using the ‘little people’ for their own ends. The likelihood that Sheppard did anything worthy of a twenty year stretch in Leavenworth? Slim to none.”

“I’m not saying he’s blameless. He disobeyed a direct order, no matter what his motive was. But I can’t stand back and let him be railroaded into something I can save him from. He’s Air Force, damn it. He’s mine…in a manner of speaking.” 

Bureaucrat though he was, Richard Woolsey had a strong sense of fair play. “What have you found to support your position, General?”

~*~

“Unscheduled activation.”

Rodney crowded John onto the floor next to the metal ring standing in front of the wall. The thing began to spin and symbols light up one by one. Coming to a stop, a cover segmented and drew back into the edges of the ring. A huge balloon of blue exploded into the room, retracting into a shimmering pool of liquid.

John took an involuntary step back from the engaging wormhole. “What?” Head spinning, he turned to the grinning McKay. “What just happened?”

“Keep watching.” Rodney practically bounced in place. “Just wait.”

With a sucking, wet sound a man stepped out of the blue and headed down the ramp. Then another. And another. With a pop the puddle disappeared and the segmented cover slid back to its place.

Rodney turned to see how John was taking the news that the Stargate was real…and more importantly, that Rodney wasn’t crazy. Smirking at the slack-jawed expression on Sheppard’s face he couldn’t resist. “Bet you can’t wait to try that yourself.”

Nodding dumbly, John snapped his mouth shut. “Rodney.” He swallowed and tried again. “We need to talk some more about Atlantis.”

~*~

Closing the file folder in front of him, General O’Neill sighed. There was no doubt in his mind that Sheppard had been the scapegoat for the sins of the CIA. Getting his superiors within the Air Force to accept that had been an exercise in masochism. He’d prevailed because he couldn’t live with the alternative. Sheppard would be reinstated as a major in good standing, on the condition that he continue on with the Atlantis expedition. O’Neill had fought that caveat. It didn’t sit well to force the man to join such a dangerous endeavor when he wasn’t going to be a prisoner anymore. The brass had decreed that since Sheppard had failed to obey orders he was due some sort of punishment. He’d retain his rank, regain his position in the command structure. To them, it was a small price to pay for that freedom.

Steeling himself, he leaned over to bellow out to Walter. “Get Sheppard and McKay in here.”

~*~

Gesturing to the SF’s hovering in their usual position just outside the door, O’Neill grinned at Sheppard. “Let’s get those shackles off, why don’t we?”

The guard stepped forward with the keys. Handing them off to O’Neill, he stepped out of the room and pulled the door closed after him. General O’Neill motioned for Sheppard to hold out his wrists. “Here we are.” He turned the key in lock, pulling the shackles away. He winced at the abraded skin exposed.

The general watched him with a smirk. “Feel good?”

“Yes, sir.” He rubbed the shackle galls on his wrists. It felt really good.

“We’ll get one of the Voodoo practitioners to give you something for those,” Rodney fretted. “You’ll be lucky not to get an infection.” He scowled at O’Neill. “The American military is made up of morons.”

“Yes, yes. Morons.” Slapping his hands together again, O’Neill smiled at John. “I suppose being stuck with McKay was marginally better than prison.” He beamed a smile at the sputtering McKay.

“We’ve been busy. As you know, I’ve been investigating your sentencing. I’ve uncovered enough to convince the Air Force to set aside your conviction. You’ll be reinstated with full military honors as of tomorrow.” He held up a hand to stop John’s questions. “Hang on for a minute. Here’s the deal. You get your career back. You get your pension back. You get back pay. But.”

Rodney reached over to put a hand on John’s arm in unconscious support.

“You’re still expected to join the Atlantis expedition. You will be acting as second-in-command to Colonel Marshall Sumner. Sumner is a marine. In fact, the military contingent joining you on the Daedalus are over 90% marines. You’ll have to win the men over. Don’t think for a minute that the story of your sentencing and parole to McKay is going to stay a secret. Ride it out. Give the men time to adjust to you. Be the officer you are and you’ll be fine.”

Clearly tired of the whole subject, he concluded. “Sumner is a hard-ass, I’m not gonna lie. But he’s a fair man and I think you’ll be able to find a way to fit in. You’ll be meeting with him Tuesday when the expedition Marines start reporting to the mountain.”

John felt his knees wobble in a way that had nothing to do with the loss of the weight of his shackles. “Yes, sir. Thank you, sir.”

Offering a text book salute, John stood as close to attention as he could manage.

Returning the salute with a seriousness that was unusual for him, O’Neill patted John on the shoulder. “At ease, Airman. You’ll be okay. Trust me.” Turning to Rodney he continued, “After the medics give him the okay to leave the infirmary, get him something to eat and check with the quartermaster about uniforms and housing.”

~*~

Finding himself in the midst of the military personnel heading for beam up to the Daedalus, John looked around to find Rodney. Though no longer tied legally to him John found he felt more grounded in his company. He’d hoped they could be friends, but Rodney had been making himself scarce since he’d been officially returned to the military. 

As promised, Colonel Sumner was a hard-ass. He’d balked at first when O’Neill had introduced Sheppard as his 2IC. After some time and conversation he’d thawed somewhat, much to John’s relief. Also as promised, it looked like the two would be able to work together.

Now if he could get things straightened out with Rodney…

Spying McKay in a cluster of blue shirts, John slipped around the perimeter of the room to cut off his escape.

“Rodney.” Rodney’s eyes grew wide as they searched for escape. “Ah, ah, ah. You’re not going to leave the gate room when the Daedalus is ready to start beaming people on board, are you? You might miss your flight.”

Slumping in defeat Rodney glared at John. “Yes, very amusing, major. Har har, very har. Was there something you needed or did you just want to demonstrate your sterling wit?”

“I want us to be friends, Rodney. I want to know why you’ve been avoiding me.”

“I haven’t been avoiding you…”

At John’s pointed glare Rodney trailed off. “Well, perhaps I _have_ been rather busy. I’m surrounded by morons, you know. We’d all be sucked out into space if the monkeys they call scientists around here were unsupervised.” Rodney shifted, “You want to us to be friends? Why? Don’t you have Air Force buddies?”

John laughed. “Air Force buddies?” Shaking his head, John reached over to clasp Rodney’s shoulder. “Yes, Rodney. I want us to be friends. You looked out for me when I needed someone to. You didn’t squawk about my return to the Force even though it meant you couldn’t bogart my Ancient gene anymore. I’m not going to throw that away. Are you?”

As Rodney struggled for words, Walter announced that beaming would begin immediately. John steered Rodney over to the group they’d both been assigned to.

“Ready, gentlemen?” O’Neill called down to the gateroom. “Good luck, and God speed.”

Rodney reached over and clamped his damp hand over John’s wrist. “No.”

“No?” Sheppard’s mobile brow lifted in confusion.

“No. I don’t want to throw it away either.”

John’s blinding smile warmed Rodney even as the transport beam swept them up. It would warm him all the way to their new home, he was sure.

~*~


End file.
